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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatggtttgtgattagtgtacaattactaagaggattgtggttgggagaaggtggcttggaacagaaaataagcttctgtggaatttcttttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATAGATGATGTCCTATATGTAGATGATA

Basic information

species Glycine max
transcript GLYMA12G02620.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g37270.2 (Oryza sativa), 3'ss of exon 3
aatggtttgtgattagtgtacaattactaagaggattgtggttgggagaaggtggcttgg----aacagaa----aataagcttctgtggaatttcttttcattg--cagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATAGATGATGTCCTATATGTAGATGATA
     | |||  ||| |     || ||| |    ||| |  |    | ||    | ||      |||| ||    ||||  | ||| |     || | ||  |||  ||||| ||||| ||||| || || || ||||| ||||| ||  ||||||||||||| ||||||||||| ||||| || ||||||||  | |||||||||||| 
-----tctgtttttaat-----atcacttaacttattctcttcaaaaaaaatcagtttactgtcaacataatcacaatattcatctttttttcttgtgtttcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCCAGAATTGATGATGTAATTTATGTAGATGATG

upper sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G105253_T03 (Zea mays), 3'ss of exon 3
------------------------------aatggtttgtgattagtgtacaattactaagaggattgtggttgggagaaggtggcttggaacagaaaataagcttctgtggaatttcttttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATAGATGATGTCCTATATGTAGATGATA
                               |    || ||   |    ||||||  ||| ||  || |  ||   |  |      |   || |   | |  | |||| || || ||          ||||||||||| ||||| || ||||||||||| ||||| ||  ||||||||||||| ||||||||||| || || || ||||||||  ||||||| |||||| 
gtaaagcctgtgcaaagacaagtaaccacctacttattctggccaaaacacaattgataa-agtctttttctttcaattacacaaatcataatattcactttgtttctttgaaaatttcc-------cagGATGTTGGGCAGTCCATACTTGAAAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCAAGAATTGATGATGTGATATATGTTGATGATG

upper sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G158679_T01 (Zea mays), 3'ss of exon 4
-------------aatggtttgtgatta-gtgtacaattactaagaggattgtggttgggagaaggtggcttgga-----acagaaaataagcttctgtggaatttcttttcattgc-agGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATAGATGATGTCCTATATGTAGATGATA
             ||       | |  | |       |  ||      ||     | |    |   |  |||  |     ||| |  | || ||||  |    ||  |     ||   ||||||| || ||||| || |||||| | || ||||| ||  ||||||||||||| ||||||||||| || || || ||||||||  | ||||| |||||| 
gtaaagctcatgcaaaaacaaataaccatggacttcttctctggccaaatcaaaatcgatcaagtctttctttcagttacacaaaccacaatcttcactttgtttcttgcgtgtttttagGATGTCGGGCAGTCCATACTTGAATGCTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCAAGAATTGATGATGTGATCTATGTTGATGATG

upper sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G38430.1 (Arabidopsis thaliana), 3'ss of exon 4
aatggtttgtgattagtgtacaattactaagaggattgtggttgggagaaggtggcttggaacagaaaataagcttctgtggaatttcttt---tcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATAGATGATGTCCTATATGTAGATGATA
                 ||||| |||      ||| |||| || |  |   |   | || |||      ||      |   || ||| | |   |  ||||||||||| || || || ||||| || ||||| || || |||||||||||| ||||||| ||||| | |||||| ||||||||||| || ||||| |||||| 
-----------------gtaca-ttatagtttggagtgtgctttgctggttgcatcatgaaacgatgcttagataatttaagagtttgtgtgtgttcttgcagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATGGCCTTCAACATCACGGCCAGAATAGATGATGTGCTTTATGTTGATGATG

upper sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g03620.t01 (Vitis vinifera), 3'ss of exon 5
aatggtttgtgattagtgtacaattactaagaggattgtggttgggagaaggtggcttgga--acagaaaataagcttctgtggaatttcttttcattg---cagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATAGATGATGTCCTATATGTAGATGATA
    ||| ||    | || | |   | ||||    ||| |  |  |      || | | ||  | |||  |||| |  ||     | || | | |||||   |||||||| || ||||| ||||| |||||||||||||| || ||||||||||| || || ||||||||||| |||||||||||||| || |||||||||||| 
----gttagtt-ccattggagaggaattaagcctcttgagaataagttgctttgacatagatgaaagatgataaccagctcatttacttatctgcattgttacagGATGTAGGGCAGTCAATTCTAGAAAGTTATTCAAGGGTAATGGAGAGCTTAGCTTTCAACATAATGGCAAGGATAGATGATGTTCTTTATGTAGATGATG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208142949|gb|GD942415.1|GD942415
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
EST: gi|193671353|gb|FK613307.1|FK613307
EST:     AGGGCTCCCTCAGACTGCACTAGATATGGACCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCT-GAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: AGGGCTCCCTCAGACTGCACTAGATATGG-CCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
EST: gi|193725025|gb|FK659277.1|FK659277
EST:     ATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: ATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
EST: gi|208294865|gb|GE093928.1|GE093928
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
EST: gi|58019995|gb|CX706737.1|CX706737
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
EST: gi|193469427|gb|FK435871.1|FK435871
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGA
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGA
EST: gi|193561483|gb|FK518994.1|FK518994
EST:     ATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTTGAAAGTTATTTCAAGAGTGATGGAGAGCT
genomic: ATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTC-TTGAAAGTTA-TTCAAGAGTGATGGAGAGCT
EST: gi|208151075|gb|GD946066.1|GD946066
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGAATGGAGAGCTT
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGA-TGGAGAGCTT
EST: gi|193707789|gb|FK646843.1|FK646843
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGA
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGA
EST: gi|208166052|gb|GD963326.1|GD963326
EST:     AGGGCTCCCTCAGACTGCACTAGATATCGGCCAAAATTCAATATAATAAG                         -ATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTT
genomic: AGGGCTCCCTCAGACTGCACTAGATAT-GGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTT
EST: gi|193514875|gb|FK470141.1|FK470141
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGG
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGG
EST: gi|193461427|gb|FK429316.1|FK429316
EST:     AGGGCTCCCTCAGACTGCACTAGATATGGACCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: AGGGCTCCCTCAGACTGCACTAGATATGG-CCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
EST: gi|208131141|gb|GD927248.1|GD927248
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTT
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTT
EST: gi|193471344|gb|FK438461.1|FK438461
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
EST: gi|208101318|gb|GD897627.1|GD897627
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGAACAAGTCTATTCTTGAAAGTTATTC
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGA-CA-GTCTATTCTTGAAAGTTATTC
EST: gi|208221462|gb|GE017296.1|GE017296
EST:     ATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: ATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
EST: gi|208136314|gb|GD940575.1|GD940575
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
EST: gi|298180826|gb|HO022265.1|HO022265
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
EST: gi|193695980|gb|FK636118.1|FK636118
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGA
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGA
EST: gi|193643776|gb|FK590809.1|FK590809
EST:     AAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: AAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
EST: gi|208268053|gb|GE072968.1|GE072968
EST:     GGGCCTCCCTCAGACTGCACTAGATATGGACCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: GGG-CTCCCTCAGACTGCACTAGATATGG-CCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
EST: gi|208195853|gb|GD993532.1|GD993532
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTT
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTT
EST: gi|193586345|gb|FK542557.1|FK542557
EST:     CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAG                         GATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG
genomic: CAGGGCTCCCTCAGACTGCACTAGATATGGCCAAAATTCAATATAATAAGgtatgttact ... ttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaaggtggcttggaacagaaaataagcttctgtggaatttcttttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATAGATGATGTCCTATATGTAGATGATA
                                       tttcttttcattgc  CT-rich tract
                                     aatttcttttcatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatggtttgtgattagtgtacaattactaagaggattgtggttgggagaaggtggcttggaacagaaaataagcttctgtggaatttcttttcattgcagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATAGATGATGTCCTATATGTAGATGATA

- - gtttgtg
- - - - - - - agtgtac
- - - - - - - - - - - - - - - - - - - -ggttggg
- - - - - - - - - - - - - - - - - - - - - - - - - -gtggctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttctg